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- PDB-6pgs: Crystal structure of bovine opsin with geraniol bound -

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Basic information

Entry
Database: PDB / ID: 6pgs
TitleCrystal structure of bovine opsin with geraniol bound
Components
  • G alpha CT2 peptide
  • Rhodopsin
KeywordsSIGNALING PROTEIN / Olfactory Receptor / Odorant
Function / homology
Function and homology information


detection of light stimulus involved in visual perception / retinal cone cell development / Opsins / VxPx cargo-targeting to cilium / rod photoreceptor outer segment / rod bipolar cell differentiation / sperm head plasma membrane / podosome assembly / absorption of visible light / opsin binding ...detection of light stimulus involved in visual perception / retinal cone cell development / Opsins / VxPx cargo-targeting to cilium / rod photoreceptor outer segment / rod bipolar cell differentiation / sperm head plasma membrane / podosome assembly / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / detection of chemical stimulus involved in sensory perception of bitter taste / : / G protein-coupled photoreceptor activity / photoreceptor inner segment membrane / rhodopsin mediated signaling pathway / 11-cis retinal binding / cellular response to light stimulus / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / phototransduction, visible light / thermotaxis / Activation of the phototransduction cascade / detection of temperature stimulus involved in thermoception / outer membrane / arrestin family protein binding / photoreceptor cell maintenance / Ca2+ pathway / photoreceptor outer segment membrane / G alpha (i) signalling events / response to light stimulus / phototransduction / photoreceptor outer segment / G-protein alpha-subunit binding / sperm midpiece / photoreceptor inner segment / visual perception / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / microtubule cytoskeleton organization / photoreceptor disc membrane / heterotrimeric G-protein complex / cell-cell junction / gene expression / G protein-coupled receptor signaling pathway / Golgi membrane / GTPase activity / GTP binding / zinc ion binding / membrane / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx ...Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Geraniol / PALMITIC ACID / Rhodopsin / Guanine nucleotide-binding protein G(t) subunit alpha-2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.905 Å
AuthorsEger, B.T. / Morizumi, T. / Ernst, O.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)Canada Research Excellence Chair Canada
CitationJournal: To Be Published
Title: Odorant-binding site in visual opsin
Authors: Morizumi, T. / Kuroi, K. / Eger, B.T. / Ou, W.L. / Van Eps, N. / Tsukamoto, H. / Furutani, Y. / Ernst, O.P.
History
DepositionJun 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhodopsin
B: G alpha CT2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7456
Polymers40,2932
Non-polymers1,4524
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint2 kcal/mol
Surface area17040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)243.919, 243.919, 109.732
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Rhodopsin /


Mass: 39031.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02699
#2: Protein/peptide G alpha CT2 peptide


Mass: 1261.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: P04696*PLUS

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Sugars , 2 types, 2 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C16H32O2
#6: Chemical ChemComp-64Z / Geraniol / Geraniol


Mass: 154.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H18O / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 7.75 Å3/Da / Density % sol: 84.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 3.1-3.3M ammonium sulfate, 0.1M sodium acetate buffer, pH 5.5

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.89→97.3 Å / Num. obs: 27357 / % possible obs: 99.3 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.034 / Rrim(I) all: 0.086 / Net I/σ(I): 16.7
Reflection shellResolution: 2.89→3.07 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.019 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4495 / CC1/2: 0.884 / Rpim(I) all: 0.509 / Rrim(I) all: 1.142 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J4Q

4j4q


Resolution: 2.905→31.206 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 1382 5.06 %
Rwork0.2123 --
obs0.2135 27336 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.905→31.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2681 0 98 0 2779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022880
X-RAY DIFFRACTIONf_angle_d0.5523918
X-RAY DIFFRACTIONf_dihedral_angle_d11.3841736
X-RAY DIFFRACTIONf_chiral_restr0.037445
X-RAY DIFFRACTIONf_plane_restr0.005475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.905-3.00860.32791280.29772546X-RAY DIFFRACTION99
3.0086-3.12890.31821570.28382561X-RAY DIFFRACTION100
3.1289-3.27120.26471370.23532590X-RAY DIFFRACTION100
3.2712-3.44340.21361360.22652605X-RAY DIFFRACTION100
3.4434-3.65890.24431390.21812593X-RAY DIFFRACTION100
3.6589-3.94090.2491430.20592600X-RAY DIFFRACTION100
3.9409-4.33650.22921230.19122598X-RAY DIFFRACTION100
4.3365-4.96190.19311380.17882626X-RAY DIFFRACTION99
4.9619-6.24320.24081380.21682583X-RAY DIFFRACTION98
6.2432-31.2060.22631430.21342652X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.68510.308-0.25021.6807-0.82081.44710.00190.11760.1216-0.1541-0.0123-0.283-0.0905-0.02750.00170.32310.0349-0.05870.28960.06710.476320.005741.94639.9464
22.21550.163-0.32830.7213-0.01670.0756-0.21970.7855-0.7377-0.7180.01190.43220.5499-0.4233-0.15770.8814-0.1375-0.07840.5133-0.04180.60367.139226.128424.6333
30.982-0.0435-0.25310.0090.14241.2185-0.37530.27610.9497-0.47090.25670.2795-0.53310.0761-0.14160.6145-0.0504-0.17570.43970.20860.657610.518149.653630.3163
42.1732-1.8053-0.35271.5307-0.13042.6547-0.09420.10540.292-0.2426-0.01540.4239-0.1079-0.35630.00010.42680.0064-0.12590.5028-0.01060.5166-1.699435.068241.8995
50.45930.09770.45210.24580.26860.4507-0.31950.0305-0.35650.57080.2826-0.17870.1437-0.1181-0.01680.6005-0.0268-0.07690.41620.00160.66213.3627.397846.7527
60.00410.0062-0.00290.0149-0.01540.0189-0.5730.208-0.248-0.80880.0592-0.04840.41730.5237-0.00071.1497-0.1058-0.10220.96610.11861.841-2.819613.865437.4781
70.00910.01210.00060.025-0.01410.01320.1956-0.16990.1419-0.21190.68980.12210.28660.37680.00050.9277-0.21170.03170.8998-0.03511.41811.615116.815140.1431
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:139)
2X-RAY DIFFRACTION2(chain A and resid 140:168)
3X-RAY DIFFRACTION3(chain A and resid 169:222)
4X-RAY DIFFRACTION4(chain A and resid 223:287)
5X-RAY DIFFRACTION5(chain A and resid 288:326)
6X-RAY DIFFRACTION6(chain B and resid 340:344)
7X-RAY DIFFRACTION7(chain B and resid 345:350)

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